Hi Eileen - It looks like there was a A-P flip introduced to your gradient
vectors. (See screenshot of the tensor eigenvectors. Because they look
right in the coronal view but wrong in the sagittal and axial views,
that's why I'm assuming the flip is in the A-P direction.) To fix this you
need to multiply the y coordinate of your gradient vectors with -1 and
rerun.
If there are still any cases of missing tracts, please look at the bottom
of your dmrirc file for instructions on how to use the reinit parameter
(or search for previous emails on that parameter in the archives).
Note that your DWI voxel size is anisotropic (finer resolution in x/y than
z), this may cause bias in tractography, so I'd recommend that you switch
to isotropic resolution for future acquisitions if you have control over
it.
Hope this helps,
a.y
On Fri, 27 Feb 2015, Eileen Moore wrote:
Hi Anastasia,
Sorry for the delay -- I missed your response. I did look at the anatomical
segmentations and thought they looked OK. I've uploaded the
tracula and corresponding freesurfer data for two subjects: one with complete
tracts and one with missing/incomplete tracts. I also
uploaded my dmrirc file. Thanks for taking a look for me.
Eileen.
Hi Eileen - Have you checked the anatomical segmentations of the subjects? The
mask that's used by default is the aparc+aseg_mask, which
comes from registering the cortical parcellationg and subcortical segmentation
from T1 to diffusion space, and then dilating it by a couple
of voxels.
If you upload an example data set for me here, I can take a look:
https://gate.nmr.mgh.harvard.edu/filedrop2/
Please include all tracula-related directories of the subject (dmri, dlabel,
etc).
Thanks!
a.y
On Thu, 18 Dec 2014, Eileen Moore wrote:
Hi - I'm having difficulty with missing or incomplete tracts most of my
subjects. I'm hoping for suggestions on where I can look for data
problems. The majority of my subjects have at least one missing/incomplete
tract, but the specific problematic tract varies across
subjects (e.g., one subject has a missing L.Uncinate; another subject has a
missing Forceps Major; another is missing the ILF bilaterally,
etc.). For my problematic tracts, the path.pd.nii.gz is a single line/curve
rather than the diffuse volumetric distribution. I'm not
sure how to correct this.
I have checked my eigenvectors -- the lines appear to be pointing in the
correct directions in my dtifit_V1 -- so I believe my gradient
table is correct
I've checked my images for motion via visual inspection and by excluding any
subjects with dwi_motion outliers in AvgTranslation,
AvgRotation, PercentBadSlices, and AvgDropoutScore.
I inspected the nodif_brain_mask.nii.gz to look for chunks of missing brain
and did not identify any problems here.
I've tried increasing the number of control points for each tract.
I'd very much appreciate any suggestions on how to troubleshoot next.
Thank you,
Eileen.
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